Adam Maybe I'm misunderstanding what you're trying to do but if you're running npm start in an empty directory nothing will happen. You need to upload your application before you can deploy it with Enhance.
The documentation doesn't mention having to upload your app (or where) before deploying the nodejs app, I just followed the Enhance NodeJS documentation to see what would happen, and apparently it starts to build something for hours. Quite different from deploying a PHP app (like wordpress) on Enhance, or deploying a NodeJS on some other panels I've tried.
This was just a testdomain website where the wordpress app was removed for this test, so I'd call that empty.